Herein, we demonstrate a strategy to improve the tensile strength, thermal safety issues, and electrochemical performance of an as-synthesized polyimide separator. By spraying the solution of a specific chemical constituent on both sides of a poly(amic acid) non-woven membrane followed by thermal treatment, a novel polyimide nanofibrous membrane with porous-layer-coated morphology was successfully fabricated by in situ self-bonding and micro-crosslinking technique. The self-bonding and micro-crosslinking techniques improve the tensile strength of the nanofiber membranes from 5 MPa to 28 MPa by forming a crosslinked network structure, thereby reducing the risk of nanofiber disassembly during long-term operation. The rigid structure and aromatic groups in the polyimide chain enable the separator to have outstanding thermal dimensional stability at temperatures as high as 300 °C and thermal stability (5% weight loss at about 528 °C). Additionally, the unique flame retarding capability of polyimide ensures high security of the battery as well. Notably, the lithium-ion battery using porous-layer-coated polyimide separator exhibits a much higher capability (129.9 mA h g⁻¹, 5C) than that using a Celgard-2400 separator (95.2 mA h g⁻¹, 5C) and could work steadily at 120 °C, thus implying promising application in next generation high-safety and high-performance lithium-ion batteries.